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The perfoliate pondweed, Potamogeton perfoliatus, is a common macrophyte in freshwater and subarctic coastal areas. This species builds extensive meadows that play a role as a filter removing nutrients traversing from land to sea and maintain essential ecosystem functions. Here, we investigated the function of perfoliate pondweed as a filter of potentially pathogenic bacteria by combining culture-dependent and 16S rRNA metabarcoding approaches. Our results suggest no significant nutrient reduction in the meadow region but the enrichment of potentially pathogenic bacteria, such as Vibrio, Legionella and Leptospira, particularly attached to macrophyte leaves. The bacterial community composition differed between seawater and macrophyte habitats, with higher relative abundances of Cyanobacteriia attached to macrophytes, without affecting alpha-diversity. The metabolic pathways of bacteria for aromatic and polymer compound degradation were enriched in the macrophytes, attributed to members of the genera Pseudorhodobacter, Novosphingobium and Erythrobacter. Functions related to such degradation suggest that the bacteria may be able to remove complex organic compounds coming from land. We argue that the macrophyte meadows may be relevant to both animal and human health, as these habitats can be hot spots for potentially pathogenic bacteria.